RosettaCommons
Error while running af2_interface_metrics.py
I've tried af2_interface_metrics.py using
But, it gave that:
core.chemical.GlobalResidueTypeSet: Total time to initialize 1.19 seconds. predict_structure(tag_buffer, feature_dict_dict, binderlen_dict, initial_guess_dict, sfd_out, scorefilename) File "/home1/LJY/rfdesign/RFDesign/scripts/af2_interface_metrics.py", line 433, in predict_structure prediction_result = jax.vmap(model_runner.apply, in_axes=(None,None,0,0))(model_runner.params, File "/home/users/LJY/.local/lib/python3.8/site-packages/jax/_src/traceback_util.py", line 163, in reraise_with_filtered_traceback return fun(*args, **kwargs) File "/home/users/LJY/.local/lib/python3.8/site-packages/jax/_src/api.py", line 1770, in vmap_f out_flat = batching.batch( File "/home/users/LJY/.local/lib/python3.8/site-packages/jax/_src/linear_util.py", line 165, in call_wrapped ans = self.f(*args, **dict(self.params, **kwargs)) File "/home/users/LJY/.local/lib/python3.8/site-packages/jax/_src/traceback_util.py", line 163, in reraise_with_filtered_traceback return fun(*args, **kwargs) File "/home/users/LJY/.local/lib/python3.8/site-packages/jax/_src/pjit.py", line 237, in cache_miss outs, out_flat, out_tree, args_flat = _python_pjit_helper( File "/home/users/LJY/.local/lib/python3.8/site-packages/jax/_src/pjit.py", line 180, in _python_pjit_helper args_flat, _, params, in_tree, out_tree, _ = infer_params_fn( File "/home/users/LJY/.local/lib/python3.8/site-packages/jax/_src/api.py", line 443, in infer_params return pjit.common_infer_params(pjit_info_args, *args, **kwargs) File "/home/users/LJY/.local/lib/python3.8/site-packages/jax/_src/pjit.py", line 520, in common_infer_params jaxpr, consts, canonicalized_out_shardings_flat = _pjit_jaxpr( File "/home/users/LJY/.local/lib/python3.8/site-packages/jax/_src/linear_util.py", line 301, in memoized_fun ans = call(fun, *args) File "/home/users/LJY/.local/lib/python3.8/site-packages/jax/_src/pjit.py", line 932, in _pjit_jaxpr jaxpr, global_out_avals, consts = pe.trace_to_jaxpr_dynamic( File "/home/users/LJY/.local/lib/python3.8/site-packages/jax/src/profiler.py", line 314, in wrapper return func(*args, **kwargs) File "/home/users/LJY/.local/lib/python3.8/site-packages/jax/interpreters/partial_eval.py", line 1985, in trace_to_jaxpr_dynamic jaxpr, out_avals, consts = trace_to_subjaxpr_dynamic( File "/home/users/LJY/.local/lib/python3.8/site-packages/jax/interpreters/partial_eval.py", line 2002, in trace_to_subjaxpr_dynamic ans = fun.call_wrapped(*in_tracers) File "/home/users/LJY/.local/lib/python3.8/site-packages/jax/_src/linear_util.py", line 165, in call_wrapped ans = self.f(*args, **dict(self.params, **kwargs)) File "/home/users/LJY/.local/lib/python3.8/site-packages/haiku/_src/transform.py", line 128, in apply_fn out, state = f.apply(params, {}, *args, **kwargs) File "/home/users/LJY/.local/lib/python3.8/site-packages/haiku/_src/transform.py", line 357, in apply_fn out = f(*args, **kwargs) jax._src.traceback_util.UnfilteredStackTrace: TypeError: _forward_fn() takes 1 positional argument but 2 were given
The stack trace below excludes JAX-internal frames. The preceding is the original exception that occurred, unmodified.
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home1/LJY/rfdesign/RFDesign/scripts/af2_interface_metrics.py", line 599, in
What can I do for this error?
sorry for nto responding to this. the af2_interface_metrics.py requires a custom AF2 version, and really should not have been included in the public release of this repo. you can get a self-contained repo for running the interface metrics here: https://github.com/nrbennet/dl_binder_design
additionally, i would encourage you to use RFDiffusion (https://github.com/RosettaCommons/RFdiffusion) instead of the hallucination/inpainting code in this repo
Thanks for the update! Yes, I just saw the RFDiffusion code. We will try designs from both tools! absolutely amazing work from the team and thanks a lot for getting back!